Brake and drivetrain issues?
 

I had to make a somewhat hard stop on my bike over the weekend and I almost fishtailed the rear end. Is that normal on a bike or do I need to use both the front and rear brakes almost simultaneously? Also, I noticed when I was in granny gear the chain was being a little chatty until I downshift the RD one click down. Could my drivetrain be out of adjustment and should I have the LBS look at it since they made the adustments when I screwed up during a cable replacement?

What you experienced is normal. Hard stops on a bike using both the front and rear brakes (which is how it should be done) will transfer enough weight forward to unload the rear wheel and may cause it to lock or skid. Skillful riders will lessen the pressure on the rear brake to minimize this.

As to the chain, were you in the granny ring and the smallest cog? That's not a proper combination and "cross chaining" is often noisy as well as not good for the chain itself.

I was in the largest rear gear and the smaller crank ring.

If you want to stop quickly, you need to use the front brake. Depending on the bike, the situation, etc., almost all of the braking is supplied by the front brake. In that situation, it does not take much rear brake to skid the rear.

From Sheldon Brown:
http://www.sheldonbrown.com/brakturn.html

OK, you were in your lowest gear, correct? The chain could be rubbing on the front derailleur cage or the chain could be not seated on the large cog. Either problem could be due to a limit screw misadjustment or a shift cable tension issue.

When I was in my granny gear, I peered down onto my crank and FD looks fine. I'm thinking the chain isn't going on the large rear cog all the way - the noise goes away when I downshift to the next cog.

I did break the chain at a non-dimpled pin and rejoined it with a OEM Shimano link a few months ago when I decided to clean the chain. I moved each link by hand to make sure they were still free.

Put the bike on a stand or somehow get the rear wheel off the ground. Then while turning the crank, try to shift the derailleur by hand to the largest cog position. If the chain seats properly on the cog, you need a cable tension adjustment. If it won't seat properly, the low limit screw is slightly too tight.